The Cypriot interior ministry said the 48 applicants for international protection were relocated from Cyprus to Germany through a European Union solidarity mechanism for voluntary relocation.
EU member Cyprus says it is at the forefront of the bloc's irregular migration flows, and last year reported the highest number of asylum applicants per capita.
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"This is the first of a series of transfers that will take place in the coming months," a ministry statement said.
It added that the transfer was undertaken "in cooperation with the European Asylum Service, the European Commission, the International Organisation for Migration and the German authorities".
The German embassy in Nicosia said the first batch of asylum seekers were from Syria and Afghanistan.
"This is the first relocation to my country - but it is only the beginning because Germany wants to take in more eligible persons soon in order to relieve the burden on Cyprus," ambassador Anke Schlimm was quoted as saying in a statement.
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The Cypriot interior ministry said the EU has worked closely with member countries to ease the burden of irregular migration, especially among those considered "frontline states".
"Germany has accepted the relocation of 500 applicants," the ministry said.
"It contributes to addressing the migration challenges faced by the Mediterranean countries, especially Cyprus," it added.
The relocations are funded by the EU and the United Nations migration agency.
Nicosia claims that asylum seekers comprise six percent of the island's population of 915,000, a record figure across the EU.
A total of 18,345 people had applied for asylum as of October, interior minister Nicos Nouris said earlier in December, compared with 13,325 for the whole of 2021.
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